Computers in Chemistry as Educa3on and Research Tools. Bong June Sung Department of Chemistry Sogang University

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1 Computers in Chemistry as Educa3on and Research Tools Bong June Sung Department of Chemistry Sogang University

Computa3onal Chemistry Computa3onal chemistry is a branch of chemistry that employs computer simula;ons based on physical principles ü Classical mechanics (Molecular dynamics

2 Computa3onal Chemistry Computa3onal chemistry is a branch of chemistry that employs computer simula;ons based on physical principles ü Classical mechanics (Molecular dynamics simula;ons) ü Quantum mechanics (Ab ini;o calcula;ons) ü Sta;s;cal thermodynamics (Monte Carlo simula;ons) Theore3cal chemistry is, on the other hand, mostly based on the mathema;cal approach

3 Topics of Computa3onal Chemistry covers almost everything Molecular Modeling using Mul3scale Simula3ons Mul3scale Systems Length Scales Bio & Complex Systems Molecular Modeling for Bio & Complex Systems Dynamics Systems Molecular Modeling using Dynamics Simula3ons Quantum Systems Molecular Modeling using Quantum Simula3ons Time Scales

4 Covers both materials and biological issues Computa;onal Chemistry confirms that new an;microbial kills E.Coli within 30 seconds, Science Daily, 2016

5 Fundamental Physical Principles Quantum Mechanics Ĥψ = Eψ ab ini;o electronic structure calcula;ons Molecular orbitals Spectra Molecular structure Chemical reac;ons Classical Mechanics! F = m a! Sta;s;cal Mechanics F = k B T ln i e E i /k B T Molecular dynamics (MD) simula;ons Macroscopic proper;es Dynamics proper;es Monte Carlo (MC) simula;ons Macroscopic proper;es Usually large systems

6 An example of Monte Carlo Simula3ons of polymer microfibers Simula;on Methods Degree of polymeriza;ons of polymers: 32 CNT Aspect Ra;o = 8 or 16 Fiber Diameter : 20 at ε= 0 CNT number density : up to 0.1 at ε= 0 Polymer number density : 0.7 at ε= 0 Experiment Methods (by Samsung) PVA, MW = SWNT 1 ~ 5 μm Fiber Diameter : 10 ~ 30 μm Fibers are produced by electrospinning

7 Computa3onal Chemistry is a general tool ACS Na3onal Mee3ng 2016 focuses on Computer & Chemistry

8 A new paradigm for educa3on Designer in Molecular World

9 Electronic structure of small molecules: an example as educa3on tools

10 Benzene as a target molecule for in-class exercise

11 Setup the simula3on: design the molecule Let s design a molecule as you wish

12 Spectrum of benzene Spectrum from the calcula3on can be used to analyze experiments

13 Vibra3on of benzene One can visualize the mo3on of atoms of a molecule

14 Molecular orbitals of benzene Orbitals (that students learn only from textbooks) can be obtained easily Our results Textbook figures

15 Conduc3vity of polymer nanofibers: an example as research tools

Stretchable Conduc3ve Materials of Ag NPs and Fibers Strain, ε = (L L 0 )/L 0 Strain represents how much the material is stretched Nanofibers with Ag NPs are s;ll conduc;ve even when ε = 0.

16 Stretchable Conduc3ve Materials of Ag NPs and Fibers Strain, ε = (L L 0 )/L 0 Strain represents how much the material is stretched Nanofibers with Ag NPs are s;ll conduc;ve even when ε = 0.6 Percola:on theory seems to match with conduc;vity measurements well Easy to build stretchable and conduc;ve tex;le-based circuits Park et al., Nature Nanotechnol. 7:803 (2012) (Samsung Electronics)

17 Nat. Mater. 10, 877 (2011) Annu. Rev. Mater. Res. 36, 333 (2006) Science (2011) Science (2005) Growing interests on polymer fiber for various its applica3on Robotics Stretchable electronics Nano Le<. 14, 1944 (2014) Nat. Nanotechnol. 7, 803 (2012) Tissue engineering Artificial muscle

Monte Carlo Simula3ons using a coarse-grained model Simula;on Methods Degree of polymeriza;ons of polymers: 32 CNT Aspect Ra;o = 8 or 16 Fiber Diameter : 20 at ε= 0 CNT number density

18 Monte Carlo Simula3ons using a coarse-grained model Simula;on Methods Degree of polymeriza;ons of polymers: 32 CNT Aspect Ra;o = 8 or 16 Fiber Diameter : 20 at ε= 0 CNT number density : up to 0.1 at ε= 0 Polymer number density : 0.7 at ε= 0 Experiment Methods (by Samsung) PVA, MW = SWNT 1 ~ 5 μm Fiber Diameter : 10 ~ 30 μm Fibers are produced by electrospinning

clusters Nanocomposites can be conduc;ve only when a

19 Electrical network needs form to be conduc3ve Connected if R < tunneling depth δ connected R disconnected Percola;ng clusters Nanocomposites can be conduc;ve only when a percola;ng electrical network forms! Periodic images Percola;ng Network

Kirchhoff s law to calculate the conductance of CNT/polymer nanocomposites contact conductance (g) btw. CNTs V=V I V=0 I R g = g 0 exp " R % #$ ξ &' ξ: tunneling characteristic length Phys. Rev.

20 Kirchhoff s law to calculate the conductance of CNT/polymer nanocomposites contact conductance (g) btw. CNTs V=V I V=0 I R g = g 0 exp " R % #$ ξ &' ξ: tunneling characteristic length Phys. Rev. B 81: (2010) V 1. Search for a percola;ng electrical network 2. Calculate the contact conductance (g) between CNTs 3. Use Kirchhoff s law with a unit poten;al and a unit current applied 4. Determine the conductance (or resistance) of overall composites

21 Rela3ve decrease in the conductance is reproduced by simula3ons λ Experiment Simula;on In both experiments and simula;ons, the conductance decreases by about 50% when ε = 50%. In both experiments and simula;ons, the decrease in rela;ve conductance is insensi;ve to the CNT concentra;on λ CNT is the line density of CNTs at ε = 0, i.e., (# of CNTs)/(Fiber Length)

22 Topology of the tunneling network changes significantly with increasing ε Network diagram for the tunneling network g > 0.7 CNT

23 Cyber Learning System based on Computa3onal Chemistry EDISON Project

24 A Cyber-Learning System : Background EDISON means EDucation-research-industry Integration through Simulation On the Net Field Experiment Virtual Experiment Crea3vity Constant Research Contents Crea3vity x+y= z Algorithm Simulation Constant Research Paper Patent Imagina3on EDISON (19c) Wherever S/W Imagina3on Movie EDISON (21c) Compu3ng Power Wherever School Home Super Computing High Performance Network 24 Anyone can learn and understand the theory or system by computer simulation anywhere and can predict operations of the system by easily changing parameters of the simulation model.

25 hops:// EDISON Project EDISON project (funded by Korean government and operated by KISTI) provides a free and internet-based educa;on soqwares You can access the soqwares anywhere in the whole world EDISON projects consists of fluid dynamics, nano science, chemistry, structural dynamics, etc.

26 EDISON_CHEM Project hops://

27 EDISON_Chem includes many so`wares for educa3on 27

Orbital/Spectrum Grid-based Simula;on of

Structure Predic;on Protein-ligand docking

Lennard-Jones par3cle of molecular dynamics

28 EDISON_Chem so`wares can be used for researches Molecular Structure/Energy/ Orbital/Spectrum Grid-based Simula;on of phase transi;ons Analysis of the structure and dynamics of polymer Analysis of the molecular structure of DNA in nanochannels Materials Modeling of Complex Systems Modeling of Biological Systems Protein Structure Predic;on Protein-ligand docking Biomolecular free energy calcula;ons Lennard-Jones par3cle of molecular dynamics SWs Design of New Molecules Structure of Colloidal Suspensions ρ

29 Thank you very much!

Nuggets on coarse- graining and mul,scale computa,onal schemes Maria Fyta Ins,tut für Computerphysik, Universität Stu<gart Stu<gart, Germany

Nuggets on coarse- graining and mul,scale computa,onal schemes Maria Fyta Ins,tut für Computerphysik, Universität Stu